Merge pull request #24 from PanDAWMS/snakemake_workflows

Snakemake workflows

pandaclient/PchainScript.py

@@ -42,27 +42,28 @@ def main():
     group_build = optP.add_group('build', 'build/compile the package and env setup')
     group_check = optP.add_group('check', 'check workflow description')
 
-
     optP.add_helpGroup()
 
     group_config.add_argument('--version', action='store_const', const=True, dest='version', default=False,
                               help='Displays version')
     group_config.add_argument('-v', action='store_const', const=True, dest='verbose', default=False,
                               help='Verbose')
     group_check.add_argument('--check', action='store_const', const=True, dest='checkOnly', default=False,
-                              help='Check workflow description locally')
+                             help='Check workflow description locally')
     group_check.add_argument('--debug', action='store_const', const=True, dest='debugCheck', default=False,
-                              help='verbose mode when checking workflow description locally')
+                             help='verbose mode when checking workflow description locally')
 
     group_output.add_argument('--cwl', action='store', dest='cwl', default=None,
                               help='Name of the main CWL file to describe the workflow')
     group_output.add_argument('--yaml', action='store', dest='yaml', default=None,
                               help='Name of the yaml file for workflow parameters')
+    group_output.add_argument('--snakefile', action='store', dest='snakefile', default=None,
+                              help='Name of the main Snakefile to describe the workflow')
 
     group_build.add_argument('--useAthenaPackages', action='store_const', const=True, dest='useAthenaPackages',
                              default=False,
                              help='One or more tasks in the workflow uses locally-built Athena packages')
-    group_build.add_argument('--vo', action='store', dest='vo',  default=None,
+    group_build.add_argument('--vo', action='store', dest='vo', default=None,
                              help="virtual organization name")
     group_build.add_argument('--extFile', action='store', dest='extFile', default='',
                              help='root or large files under WORKDIR are not sent to WNs by default. '
@@ -85,7 +86,7 @@ def main():
                               help='Suppress email notification')
     group_submit.add_argument('--prodSourceLabel', action='store', dest='prodSourceLabel', default='',
                               help="set prodSourceLabel")
-    group_submit.add_argument('--workingGroup', action='store', dest='workingGroup',  default=None,
+    group_submit.add_argument('--workingGroup', action='store', dest='workingGroup', default=None,
                               help="set workingGroup")
 
     group_expert.add_argument('--intrSrv', action='store_const', const=True, dest='intrSrv', default=False,
@@ -105,10 +106,23 @@ def main():
     options = optP.parse_args()
 
     # check
-    for arg_name in ['cwl', 'yaml', 'outDS']:
+    if options.cwl:
+        workflow_language = 'cwl'
+        workflow_file = options.cwl
+        workflow_input = options.yaml
+        args_to_check = ['yaml', 'outDS']
+    elif options.snakefile:
+        workflow_language = 'snakemake'
+        workflow_file = options.snakefile
+        workflow_input = ''
+        args_to_check = ['outDS']
+    else:
+        tmpLog.error('argument --cwl or --snakefile is required')
+        sys.exit(1)
+
+    for arg_name in args_to_check:
         if not getattr(options, arg_name):
-            tmpStr = "argument --{0} is required".format(arg_name)
-            tmpLog.error(tmpStr)
+            tmpLog.error('argument --{0} is required'.format(arg_name))
             sys.exit(1)
 
     # check grid-proxy
@@ -139,8 +153,9 @@ def _onExit(dir, del_command):
     archiveName = 'jobO.%s.tar.gz' % MiscUtils.wrappedUuidGen()
     archiveFullName = os.path.join(tmpDir, archiveName)
     extensions = ['cwl', 'yaml', 'json']
-    find_opt = ' -o '.join(['-name "*.{0}"'.format(e) for e in extensions])
-    tmpOut = MiscUtils.commands_get_output('find . {0} | tar cvfz {1} --files-from - '.format(find_opt, archiveFullName))
+    find_opt = ' -o '.join(['-name "*.{0}"'.format(e) for e in extensions] + ['-name "Snakefile"'])
+    tmpOut = MiscUtils.commands_get_output(
+        'find . {0} | tar cvfz {1} --files-from - '.format(find_opt, archiveFullName))
 
     if options.verbose:
         print(tmpOut + '\n')
@@ -177,9 +192,9 @@ def _onExit(dir, del_command):
     params = {'taskParams': {},
               'sourceURL': sourceURL,
               'sandbox': archiveName,
-              'workflowSpecFile': options.cwl,
-              'workflowInputFile': options.yaml,
-              'language': 'cwl',
+              'workflowSpecFile': workflow_file,
+              'workflowInputFile': workflow_input,
+              'language': workflow_language,
               'outDS': options.outDS,
               'base_platform': os.environ.get('ALRB_USER_PLATFORM', 'centos7')
               }